[3dem] fc4i defect
Maarten Tuijtel
maarten.tuijtel at biophys.mpg.de
Wed Jan 24 00:41:37 PST 2024
Dear Ji-Joon & Jin Young,
On our Falcon4i, we have 3 defect pixel lines and we are succesfully
using it for both single-particle and cryo-ET.
However, we noticed that it is important that the dose-rate at which the
gain reference is acquired should roughly match the dose-rate used
during data-collection. Luckily, there is still quite some variability
in dose-rate where the gain reference works well.
Hope that helps,
Maarten
Maarten Tuijtel PhD
Postdoctoral Researcher
Department of Molecular Sociology
Room B1.105
Max Planck Institute of Biophysics
Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
Office phone number: +4969 6303 3508
On 24/01/2024 09:24, Ji-Joon Song wrote:
> Hi Daniel,
> Yes, we tried all possible combinations for the gain rotation/flipping.
> Thanks,
>
> Ji-Joon
>
>
> *===============*
>
> *Ji-Joon Song, Ph.D.*
>
>
> *Professor*
>
> *Dep. Biological Sciences*
>
> *KAIST, Korea*
>
> *songj at kaist.ac.kr*
>
> *jijoonsong.kaist at gmail.com* <mailto:jijoonsong.kaist at gmail.com>
>
> *https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!Fu73VckZQ1AFdWTlfJV9W7Qfuhl59aPYkMOF8BPyuybnmQb1M3_zABJ4KRNzenM6G2K0LvBCJyNAvyXCWzUxprghLCEor-dGFhEb$
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>
>
> *Song-KAIST ZOOM link:*
>
> *https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!Fu73VckZQ1AFdWTlfJV9W7Qfuhl59aPYkMOF8BPyuybnmQb1M3_zABJ4KRNzenM6G2K0LvBCJyNAvyXCWzUxprghLCEorz_WkEOs$
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>
> *===============*
>
>
>
>
> -----Original Message-----
> From: "Daniel Asarnow" <asarnow at msg.ucsf.edu>
> To: "Ji-Joon Song" <songj at kaist.ac.kr>;
> Cc: "Jin Young Kang" <jykang59 at kaist.ac.kr>; "Takanori Nakane"
> <tnakane.protein at osaka-u.ac.jp>; "3dem at ncmir.ucsd.edu"
> <3dem at ncmir.ucsd.edu>; "김나윤" <nayunkim at kaist.ac.kr>;
> Sent: 2024-01-24 (We) 17:21:26 (UTC+09:00)
> Subject: Re: [3dem] fc4i defect
>
> Hi Ji-Joon,
> Just wanted to ask - have you tried all possible values for the gain
> rotation / flipping?
>
> Best,
> -da
>
> On Wed, Jan 24, 2024 at 12:08 AM Ji-Joon Song <songj at kaist.ac.kr> wrote:
>
> !-------------------------------------------------------------------|
> This Message Is From an External Sender
> This message came from outside your organization.
> |-------------------------------------------------------------------!
>
> You meant actual gainreference.mrc.
> I will try what you suggest and will get you back shorlty.
> Many thanks,
>
> JI-Joon
>
>
>
>
> ===============
>
> Ji-Joon Song, Ph.D.
>
>
> Professor
>
> Dep. Biological Sciences
>
> KAIST, Korea
>
> songj at kaist.ac.kr
>
> jijoonsong.kaist at gmail.com
>
>
>
> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYtD0yt34$
>
>
>
>
>
> Song-KAIST ZOOM link:
>
> https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYVka3Gs0$
>
>
> ===============
>
>
>
>
> -----Original Message-----
> From: "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>
> To: "Ji-Joon Song" <songj at kaist.ac.kr>; "Jin Young Kang"
> <jykang59 at kaist.ac.kr>;
> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> Sent: 2024-01-24 (We) 16:57:06 (UTC+09:00)
> Subject: Re: [3dem] fc4i defect
>
> Hi,
>
> > Even if we put defect file having two columns as defects,
> supposing
> that this will mask the two defect lines, this does not always
> work. The
> lines sometime continue to appear depending on data sets.
>
> "defect file": do you mean a text file that can be specified apart
> from
> a gain reference?
>
> Did you inspect the gain reference and modify it as I suggested?
> If not, please do so.
>
> I cannot comment on CryoET as I don't do it at all.
>
> > Is this a kind of a bad detector that TFS definitely should
> replace?
>
> It is almost impossible (economically) to make a perfect, defect free
> detector. Each manufacturer defines a maximum limit of defects for
> an "acceptable" chip.
>
> "The TF manufacturer claims that the detector is within their spec."
> suggests that these two lines are within their spec and they are not
> willing to replace it, unfortunately.
>
> The situation is the same as hot and dead pixels on an LCD monitor.
>
> From a developer's perspective, I hope detector software to fill
> defective pixels. Different detectors have different defect patterns.
> For example, Gatan's K2 detectors tend to have strange 3x3 blobs
> (as mentioned in the MotionCor2 paper) but rarely have
> line defects. I don't want to implement detector specific correction
> algorithms in RELION. This should be handled by the detector software.
>
> Best regards,
>
> Takanori Nakane
>
> On 2024/01/24 16:43, Ji-Joon Song wrote:
> > Hi Takanori,
> >
> > it is not straightforward.
> > Even if we put defect file having two columns as defects,
> supposing that this will mask the two defect lines, this does not
> always work. The lines sometime continue to appear depending on
> data sets.
> > In addition, as Jin Young raised an issue, we are more concerned
> about cryo-ET.
> > Is this a kind of a bad detector that TFS definitely should replace?
> > Many thanks,
> >
> > Ji-Joon
> >
> >
> >
> > ===============
> >
> > Ji-Joon Song, Ph.D.
> >
> >
> > Professor
> >
> > Dep. Biological Sciences
> >
> > KAIST, Korea
> >
> > songj at kaist.ac.kr
> >
> > jijoonsong.kaist at gmail.com
> >
> >
> >
> >
> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYtD0yt34$
>
> >
> >
> >
> >
> > Song-KAIST ZOOM link:
> >
> >
> https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!E4woV4DSHJ800rZRXPzLnrk77xiWzhQmbkQ0S_mvT8BSLknZI7HICqDtg1CnGlqUktjVZFBBYdfYVka3Gs0$
>
> >
> > ===============
> >
> >
> >
> >
> > -----Original Message-----
> > From: "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>
> > To: "Jin Young Kang" <jykang59 at kaist.ac.kr>; "Ji-Joon Song"
> <songj at kaist.ac.kr>;
> > Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> > Sent: 2024-01-24 (We) 16:15:39 (UTC+09:00)
> > Subject: Re: [3dem] fc4i defect
> >
> > Hi,
> >
> > Did you check the gain values on the white line and the gray line?
> > Is white 0? If so, making the gray line 0 will also mask it,
> > at least on RELION. I don't know how other programs handle defects.
> >
> > Best regards,
> >
> > Takanori Nakane
> >
> > On 2024/01/24 16:08, Jin Young Kang wrote:
> >> Hi Takanori and 3dem community,
> >>
> >>
> >> I hope everyone is well. I wanted to join the discussion
> Ji-Joon raised in our 3dem community. I thank Ji-Joon for raising
> this important topic.
> >> I'm part of the same institute as Ji-Joon, and I share his
> concerns about the potential impact of a certain defect,
> particularly in the context of cryo-ET.
> >>
> >> Our data analysis has revealed some peculiar 2D classes with
> particles clustering along the defect line. Unfortunately, due to
> the defect's central location on the display, we anticipate a
> significant loss of particles. However, for single particle
> analysis, we do have the option to exclude these unusual particle
> images (I attached a figure showing this).
> >>
> >> However, how about cryo-ET? Given that the defect is situated
> in the central area, avoiding it during data collection is not
> feasible. This is especially concerning as, during cryo-ET, we
> need to capture tilt series, where objects undergo substantial
> movement with varying tilt angles. This raises questions about the
> quality of the data we can obtain.
> >>
> >> Our resource center staff have invested a significant amount of
> effort in establishing a state-of-the-art 300keV cryo-EM facility
> on campus, and we are determined to make the most of this valuable
> resource. Therefore, we are eager to find a solution that ensures
> we can collect the highest quality cryo-ET data without the
> interference of defects.
> >>
> >> I would appreciate your valuable insights and advice on how we
> can effectively address this issue. Your expertise and
> perspectives would be greatly appreciated in helping us optimize
> the use of our cryo-EM facility and advance our research goals.
> (Of course, if possible, we would like to request a new camera
> chip...)
> >>
> >> Thank you in advance for your contributions to this discussion,
> and I look forward to hearing your thoughts on this matter.
> >>
> >> Best regards,
> >> Jin Young
> >>
> >>
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: "Ji-Joon Song" <songj at kaist.ac.kr>
> >> To: "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>;
> >> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> >> Sent: 2024-01-24 (We) 13:39:56 (UTC+09:00)
> >> Subject: Re: [3dem] fc4i defect
> >>
> >> Thanks!
> >> We will look into it more.
> >> Best,
> >>
> >> JI-Joon
> >>
> >>
> >>
> >>
> >> ===============
> >>
> >> Ji-Joon Song, Ph.D.
> >>
> >>
> >> Professor
> >>
> >> Dep. Biological Sciences
> >>
> >> KAIST, Korea
> >>
> >> songj at kaist.ac.kr
> >>
> >> jijoonsong.kaist at gmail.com
> >>
> >>
> >>
> >>
> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$
> >>
> >>
> >>
> >>
> >> Song-KAIST ZOOM link:
> >>
> >>
> https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$
> >>
> >> ===============
> >>
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: "Takanori Nakane" <tnakane.protein at osaka-u.ac.jp>
> >> To: "Ji-Joon Song" <songj at kaist.ac.kr>;
> >> Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> >> Sent: 2024-01-24 (We) 13:35:53 (UTC+09:00)
> >> Subject: Re: [3dem] fc4i defect
> >>
> >> Hi,
> >>
> >> > can you inform me how I can set defective lines to have 0s
> in the
> >> gain reference?
> >>
> >> If the camera software is aware of the defect lines,
> >> the values in the gain reference should be zero.
> >> But different versions of the camera software may behave
> differently.
> >> Please ask your TFS support staff.
> >>
> >> Alternatively, you can read the gain reference (.gain is a TIFF
> file),
> >> set 0, and write it back by a simple Python script.
> >>
> >> Best regards,
> >>
> >> Takanori Nakane
> >>
> >> On 2024/01/24 13:31, Ji-Joon Song wrote:
> >>>
> >>> Hi Takanori,
> >>>
> >>> Thank you for the info.
> >>> Do you mean to set 0s to the defected pixels (lines) at a
> defect file?
> >>> or can you inform me how I can set defective lines to have 0s
> in the gain reference?
> >>> Thanks in advance.
> >>>
> >>> Ji-Joon
> >>>
> >>>
> >>>
> >>>
> >>> ===============
> >>>
> >>> Ji-Joon Song, Ph.D.
> >>>
> >>>
> >>> Professor
> >>>
> >>> Dep. Biological Sciences
> >>>
> >>> KAIST, Korea
> >>>
> >>> songj at kaist.ac.kr
> >>>
> >>> jijoonsong.kaist at gmail.com
> >>>
> >>>
> >>>
> >>>
> https://urldefense.com/v3/__http://www.song-kaist.org__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_iXRP1DQ$
> >>>
> >>>
> >>>
> >>>
> >>> Song-KAIST ZOOM link:
> >>>
> >>>
> https://urldefense.com/v3/__https://kaist.zoom.us/j/89910489123__;!!Mih3wA!DC-yynt5LWW4Z-e7kinGQehHaAg81rMV5ovTKloDhavQM7hY4PEpylZTYNmA8iG-Rg2hamgd51C_3zivYY0$
> >>>
> >>> ===============
> >>>
> >>>
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: "tnakane.protein at osaka-u.ac.jp"
> <tnakane.protein at osaka-u.ac.jp>
> >>> To: "Ji-Joon Song" <songj at kaist.ac.kr>;
> "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>;
> >>> Cc:
> >>> Sent: 2024-01-24 (We) 10:30:09 (UTC+09:00)
> >>> Subject: Re: [3dem] fc4i defect
> >>>
> >>> Hi,
> >>>
> >>>> Our institute recently installed a brand new Titan krios with
> Facon4i.
> >>>> But, we are having an issue in the detector as there are two
> consecutive lines of defect in the detector.
> >>>> When we acquire and motioncorr micrographs, we have a thick
> black line as attached.
> >>>> This line sometimes disappears when we use specific programs
> such as CryoSparc but not working Relion.
> >>>> The TF manufacturer claims that the detector is within their
> spec.
> >>>> I would like to request any advice regarding this issue.
> >>>
> >>> Please make sure pixels on these defective lines have 0s in
> the gain reference.
> >>> RELION tries to conceal defects by randomly picking values
> from a good pixel nearby.
> >>>
> >>> That being said, information on defective pixels is lost and
> cannot be recovered.
> >>> Defect correction only conceals, not fixes, the problem.
> >>> In my experience, one can throw away all particles on a
> defective line and the resolution does not change much.
> >>>
> >>> Best regards,
> >>>
> >>> Takanori Nakane
> >> _______________________________________________
> >> 3dem mailing list
> >> 3dem at ncmir.ucsd.edu
> >>
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